tbuckley/cabot-search huggingface dataset:
Natural language processing-optimized case selection for real-world evidence studies.
Authors: Jacob Koskimaki, Jenny Hu, Yiduo Zhang, Jose Mena, Nehanda Jones, Elizabeth Lipschultz, Vivek Prabhakar Vaidya, Gabriel Altay, Vance Andrei Erese, Krishna Kumar Swaminathan, Emma Mendonca, Tarun Dutt, Kuldeep Singh, Tian King, Vinay Phani Santosh Lakkimsetty, Hussein Al-Olimat, Brittany Manning, George Anthony Komatsoulis, Simon Chu, Jeff Ottens
Journal: Journal of Clinical Oncology (2022)

1556 Background: Much information describing a patient’s cancer treatment remains in unstructured text in electronic health records and is not recorded in discrete data fields. Accurate data completeness is essential for quality care improvement and research studies on de-identified patient records. Accessing this high-value content often requires manual and extensive curation review. Methods: AstraZeneca, CancerLinQ, ConcertAI, and Tempus have developed a natural language processing (NLP)-assisted process to improve clinical cohort selection for targeted curation efforts. Hybrid, machine-learning model development included text classification, named entity recognition, relation extraction and false positive removal. A subset of nearly 60,000 lung cancer cases were included from the CancerLinQ database, comprised of multiple source EHR systems. NLP models extracted EGFR status, stage, histology, radiation therapy, surgical resection and oral medications. Based on the results, cases were selected for additional manual curation, where curators confirmed findings of the NLP-processed data. Results: NLP methods improved cohort identification. Successfully returned cases using the NLP method ranged from 75.2% to 96.5% over more general case selection criteria based on limited structured data. For all cohorts combined, 84.2% of the cases sent out for NLP curation were returned with curated content (Table). Each cohort contained a range of NLP-derived elements for curators to further review. In comparison, more general case selection criteria yielded a total of 3,878 cases returned out of 41,186 lung cancer cases sent for curation, for a success rate of only 9.6%. Conclusions: NLP-driven case selection of six distinct, complex lung cohorts resulted in an order of magnitude improvement in eligibility over candidate selection using structured EHR data alone. This study demonstrates NLP-assisted approaches can significantly improve efficiency in curating unstructured health data. [Table: see text]
Table of Contents
Authors: Pavel Kolkhir, Melba Mun ˜oz, Riccardo Asero, Marta Ferrer, Emek Kocatu ¨rk, Martin Metz, Yi-Kui Xiang, Marcus Maurer, Francesca Levi-Schaffer, Bernhard Gibbs, Jenny Hallgren, Carlo Pucillo, Frank Redegeld, Frank Siebenhaar, Joana Vitte, Soraya Mezouar, ¨se Michel, Giorgio Puzzovio, Mindy Tsai, Peter Valent, Stephen Galli, Michel Arock, Gregor Hoermann, Karl Sotlar, Olivier Hermine, Wolfgang Sperr, Karin Hartmann, Knut Brockow, Cem Akin, Massimo Triggiani, Sigurd Broesby-Olsen, Andreas Reiter, Jason Gotlib, Hans-Peter Horny, Alberto Orfao, Dean Metcalfe, Lina Degenfeld-Schonburg, Dubravka Smiljkovic, Martin Steinhoff, Fareed Ahmad, Atul Pandey, Angeliki Datsi, Ayda Alhammadi, Sara Al-Khawaga, Aysha Al-Malki, Jianghui Meng, Majid Alam, Joerg Buddenkotte, Hywel Williams, Jochen Schmitt, Kim Thomas, Phyllis Spuls, Eric Simpson, Christian Apfelbacher, Joanne Chalmers, Masutaka Furue, Norito Katoh, Louise Gerbens, Yael Leshem, Laura Howells, Jasvinder Singh, Maarten Boers, Leanne Van Leeuwen, Corine Geurtsvankessel, Pauline Ellerbroek, Godelieve De Bree, Judith Potjewijd, Abraham Rutgers, Hetty Jolink, Frank Van De Veerdonk, Eric Van Gorp, Faye De Wilt, Susanne Bogers, Lennert Gommers, Daryl Geers, Anke Bruns, Helen Leavis, Jelle Van Haga, Bregtje Lemkes, Annelou Van Der Veen, S De Kruijf-Bazen, Pieter Van Paassen, Karina De Leeuw, Annick Van De Ven, Petra Verbeek-Menken, Annelies Van Wengen, Sandra Arend, Anja Ruten-Budde, Marianne Van Der Ent, P Martin Van Hagen, Rogier Sanders, Marloes Grobben, Karlijn Van Der Straten, Judith Burger, Meliawati Poniman, Stefan Nierkens, Marit Van Gils, Rory De Vries, Virgil Dalm, Aaron Miller, Nicholas Rider, Richard Pyles, Barbara Judy, Xuping Xie, Pei-Yong Shi, Thomas Ksiazek, Nils Jo ˜gi, Negusse Kitaba, Torgeir Storaas, Vivi Schlu ¨nssen, Kai Triebner, John Holloway, William Horsnell, Cecilie Svanes, Randi Bertelsen, Vamsi Guntur, Laurie Manka, Camille Moore, Elizabeth Wynn, Eszter Vladar, Rafeul Alam, Tuyet-Hang Pham, Tasha Fingerlin, Richard Martin, Gaithersburg Colo, Mengyuan Kan, Avantika Diwadkar, Haoyue Shuai, Jaehyun Phd, Alberta Wang, Joanne Sordillo, Carlos Iribarren, Natalia Hernandez-Pacheco, Javier Perez-Garcia, Mario Gorenjak, Esteban Burchard, Maria Pino-Yanes, Ann Wu, Blanca Himes, Helena Bui, Amena Keshawarz, Shih-Jen Hwang, Chen Phd, Gha Lee, Kathryn Recto, George O'connor, Polina Pyatilova, Tameem Ashry, Qingqing Jiao, Teresa Abad-Perez, Sabine Altrichter, Carolina Vera, Martin Church, Jiajun He, Katharina Lohse, Jo Scheffel, Tu ¨rk, Stefan Frischbutter, Marcus Md, Lori Broderick, Gwendolyn Clay, Robert Blum, Yang Liu, Rachael Mcvicar, Fabio Papes, Laela Booshehri, Ian Cowell, Caroline Austin, Christopher Putnam, Dan Kaufman, Miles Weinberger, William Hardie
Journal: Journal of Allergy and Clinical Immunology (2022)
Disparities in timely treatment among lung cancer patients.
Authors: Jatin Chhabra, Herman Ray, Sergii Derkach, David Thompson, Warren Whyte
Journal: Journal of Clinical Oncology (2022)

e18515 Background: NSCLC is the leading cause of cancer-related deaths in the US. There are no federal standardized guidelines regarding timely treatment (TT) of NSCLC care and little is known regarding the sociodemographic differences in TT of anticancer therapies among NSCLC patients. This is particularly notable among Black Americans, who are less likely to receive lung cancer screening, more likely to be diagnosed with advanced or metastatic NSCLCL, and less likely to receive NCCN-concordant targeted therapy relative to their white counterparts. The objective of this retrospective study is to assess racial differences in TT and related outcomes among patients with advanced or metastatic NSCLC (aNSCLC). Methods: We identified 3,603 patients from ConcertAI’s Real-world data (RWD) sources, including CancerLinQ Electronic Medical Records. Patient demographics included: a) aged 18 to 64 years; b) confirmed diagnosis of aNSCLC between January 1, 2010, and December 31, 2019; and c) self-identify as White or African American. For this study the primary endpoint was receipt of TT, defined as start of systemic therapy within 30 days after diagnosis of aNSCLC. Logistic regression was leveraged to obtain adjusted odds ratios of comparisons between White and Black American populations on receipt of TT, controlling for demographic and baseline characteristics such as type of setting, ECOG score and smoking status. Results: Descriptive analyses revealed 79.1% of Black aNSCLC patients did not receive TT, as compared to 71.4% of White aNSCLC patients. When controlling for associated confounding factors, Black aNSCLC patients had a 21.4% less chance of receiving TT as compared to White patients, and the same was evident from the predicted probabilities of TT for Black vs. White aNSCLC patients. When evaluating institutional setting type, 76.1% of community hospitals provided TT vs. 61.3% of academic centers. Conclusions: This real-world study shows Black aNSCLC patients were associated with treatment delay. While present findings suggest improving access to effective screening and timely access to NCCN-concordant targeted therapies may be used as a means through which to lessen NSCLC disparities, further investigation is required to assess how it may improve overall outcomes for minorities. [Table: see text]
LGG-04. Clinical and molecular characterization of metastatic pediatric low grade gliomas
Authors: Holly Lindsay, Austin Stuckert, Murali Chintagumpala, Jack Su, Patricia Baxter, M Fatih Okcu, Fatema Malbari, Surya Rednam, Jacquelyn Reuther, Kevin Fisher, Sarah Scollon, Sharon Plon, Angshumoy Roy, D Will Parsons, Frank Lin
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND: Despite being the most common central nervous system tumor in children, ≤5% of pediatric low grade gliomas (pLGG) present with metastases. Due to their rarity, there is a paucity of clinical and molecular data in metastatic pLGGs. To address the need, we analyzed a cohort of 22 patients with pLGG followed at Texas Children’s Hospital who presented with metastatic disease. RESULTS: The predominant histology was pilocytic astrocytoma (16/22, 73%); average age at diagnosis was 4 years 11 months. The most common sites of primary disease were optic pathway/chiasm (7/22, 32%) and suprasellar (5/22, 23%). Metastatic disease was most commonly noted in the leptomeninges (12/22, 55%). 16/22 patients (73%) were treated with up-front medical therapy following tumor biopsy/resection, the majority with carboplatin-based therapy; the remaining 6 patients received only surgery up-front. Only 2/22 patients (9%) did not progress after their initial treatment with an average follow-up of 42 months. 14 patients (14/22, 64%) had continued disease progression after at least 2 therapeutic interventions; however, only 3 patients (3/22, 14%) eventually received craniospinal radiation. 10 patients (10/22, 45%) received treatment with an agent targeting the mitogen-activated protein kinase (MAPK) pathway. 20/22 patients (91%) were alive at last follow-up (average 72 months). 4/21 patients (19%) harbored a BRAF V600E mutation while 7/20 (35%) had a BRAF::KIAA1549 duplication/fusion. 8/20 patients (40%) were wildtype for both analyzed molecular alterations in BRAF. 8 patients had germline whole exome sequencing performed and all were negative for pathogenic/likely-pathogenic variants related to their clinical phenotype. Methylation analyses are pending on patients with available tumor tissue. CONCLUSION: In our cohort of patients with metastatic pLGG, most tumors progressed despite numerous therapeutic regimens, but the overall survival was &amp;gt;90%. 40% of patients were wild type for the 2 most common MAPK alterations seen in pLGG.
Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses
Authors: Wan-ting He, Rami Musharrafieh, Ge Song, Katharina Dueker, Longping V. Tse, David R. Martinez, Alexandra Schäfer, Sean Callaghan, Peter Yong, Nathan Beutler, Jonathan L. Torres, Reid M. Volk, Panpan Zhou, Meng Yuan, Hejun Liu, Fabio Anzanello, Tazio Capozzola, Mara Parren, Elijah Garcia, Stephen A. Rawlings, Davey M. Smith, Ian A. Wilson, Yana Safonova, Andrew B. Ward, Thomas F. Rogers, Ralph S. Baric, Lisa E. Gralinski, Dennis R. Burton, Raiees Andrabi
Journal: Nature Immunology (2022)
Real-world survival outcomes associated with use of pertuzumab and trastuzumab emtansine (T-DM1) for HER2-positive (HER2+) metastatic breast cancer (MBC) in Brazilian private healthcare setting.
Authors: Rodrigo Dienstmann, Heloisa Cruz, Aline Coelho Gonçalves, Diocesio Alves Pinto de Andrade, Pedro Emanuel Rubini Liedke, Rafael Brant Costa, Mario Alberto Dantas Loures da Costa, Alexandre Boukai, Flavia Rocha Paes, Luciana G. Landeiro, Daniel Luiz Gimenes, Maria Cristina Figueroa Magalhaes, Cristiano Augusto Andrade de Resende, Tomas Reinert, Pedro N. Aguiar Junior, Rafael Paes, Matheus Costa e Silva, Bruno Lemos Ferrari, Max S. Mano
Journal: Journal of Clinical Oncology (2022)

e13022 Background: Breast cancer is a leading death cause of women in Brazil. There are increased concerns with limited access to innovative therapies and the effectiveness of these agents outside clinical trials. This study aims to assess practice patterns and real-world outcomes of patients with HER2+ metastatic breast cancer (MBC) treated in the largest network of community oncology practices of Brazil after the introduction of pertuzumab and T-DM1 in routine care. Methods: De-identified electronic medical records from Oncoclínicas Group were aggregated in a cloud-based central database that allows technology-based abstraction, whereby trained data curators qualify the information using mCODE standards. We included data from all patients with a confirmed diagnosis of HER2+ MBC treated from 2014 to 2021. The primary objective was median overall survival (OS) from diagnosis of metastatic disease and other endpoints included adoption of pertuzumab-based regimen and T-DM1 in the palliative setting and their median Time to Treatment Discontinuation (TTD) in a real-world scenario. Results: Out of 21,559 patients with BC in our database, 6,215 had HER2+ disease and 1,250 had MBC treated with at least one palliative anti-HER2 therapy. Median age at diagnosis was 56 years, 29% had de novo metastatic disease, 81% received 2 nd line therapy and 47% a 3 rd line or beyond. With a median follow-up of 2 years, median OS was 49 months (CI95% 44-59). We found a ten-fold increase in the proportion of patients receiving pertuzumab or T-DM1 in the last two years when compared to 2014-2015. Overall, 62% received a pertuzumab-based regimen, mostly in the 1st line (76%), with median TTD of 9.9 months (CI95% 9-13). T-DM1 was accessible to 22% of the patients, mostly in 2nd (28%) or 3rd line and beyond (50%), with median TTD of 10.2 months (CI95% 9-13). Conclusions: In the largest Brazilian real-world study of patients with HER2+ MBC treated in the private health system, we found similar outcomes as those reported in North-American and European cohorts, both in terms of OS and TTD with standard-of-care therapies. Adoption of pertuzumab and T-DM1 was fast, but there are still gaps in access and the need to optimize clinical positioning of new anti-HER2 therapies recently approved for clinical use.
Developing of a novel nephrometry score to predict the outcomes of percutaneous ablation of renal masses: The PCT score
Authors: A. Uleri, P. Diana, E. Beatrici, G. Lughezzani, D. Poretti, F. D'Antuono, M. Lazzeri, R. Hurle, A. Saita, P. Casale, R. Contieri, V. Fasulo, V. Pedicini, N. Buffi
Journal: European Urology (2022)
Trends in treatment patterns associated with small cell lung cancer in a U.S. Medicare population.
Authors: Robert A. Ramirez, Marley Boyd, Paul Cockrum
Journal: Journal of Clinical Oncology (2022)

8584 Background: Characterizing changes in the incident small cell lung cancer (SCLC) patient population and SCLC treatment landscape is essential for understanding drivers of outcomes among patients diagnosed with SCLC. The objective of this study was to examine trends in patient characteristics and treatment patterns for SCLC in a Medicare population. Methods: A retrospective analysis was conducted using the Surveillance, Epidemiology, and End Results (SEER)–Medicare linked data. Patients were included if they had a record with a diagnosis of SCLC in the database from 1/1/2007 – 12/31/2017 and were ≥65 years of age at diagnosis. Patients also had continuous enrollment for ≥180 days pre-SCLC diagnosis. Characteristics and treatment patterns were stratified by year of SCLC diagnosis. Results: 13,516 patients met the study criteria. Overall, 57.7% were female, mean age was 74 years, 89.5% were white, and 45.6% had a history of tobacco use. The majority (73.1%) were diagnosed with stage IV disease. Just over half (55.4%) of patients initiated first line (1L) treatment and mean time from diagnosis to 1L treatment was 6 weeks. Only 36.7% of those initiating 1L went on to second line (2L). Platinum-based chemotherapy (carboplatin or cisplatin + etoposide) was by far the most common 1L regimen (91.3%). 44.7% of patients received monotherapy in 2L, with topotecan being the most common (28.4%) regimen. Carboplatin + etoposide was used for approximately 20% of 2L patients. Over time, the demographic characteristics of patients diagnosed with SCLC was fairly stable with the exception of patients reporting a history of tobacco use, which more than tripled, increasing from 19.3% to 67.7% between 2007 and 2017. Between 2007 and 2017 the share of SCLC patients initiating 1L treatment increased 8.2% from 53.8% to 58.2% and the share initiating 2L fluctuated between 35% and 39%. Platinum-based chemotherapy was consistently used by the vast majority (88.7%–96.6%) of patients in 1L during the study period. Other chemo monotherapy (e.g., topotecan) and platinum-based chemotherapy with or without irinotecan were the most common 2L regimens from 2007-2014. Use of checkpoint inhibitors (CPIs) in 2L began in 2015 and became the most common 2L treatment following platinum-based chemotherapy by 2017 with 41.5% of patients receiving a CPI in 2L. Conclusions: While an increasing share of SCLC patients are pursuing treatment, less than 60% of SCLC patients receive any anticancer therapy. Fewer still receive more than one line of treatment, highlighting the ongoing need for effective therapies for SCLC.
Development and validation of the metric-based assessment of a robotic dissection task on an avian model
Authors: S. Puliatti, M. Amato, E. Mazzone, G. Rosiello, R. De Groote, C. Berquin, P. Piazza, R. Farinha, L.P. Boret, E. Van Respaille, L. Wittouck, S. Micali, A. Mottrie, A. Gallagher
Journal: European Urology (2022)
Quality of life in caregivers of cancer patients in Colombia.
Authors: Daniela A. Castro-Martinez, Laura X. Ruiz-Cabrera, Leonardo Mariño-Ramírez, Henry Idrobo
Journal: Journal of Clinical Oncology (2022)

e24000 Background: It is well known that improvements in caregiver quality of life (QOL) could significantly impact the clinical outcome of cancer patients, which is why it is essential to study this population. Caregivers have extensive responsibilities, making them vulnerable to emotional, physical, social, and financial distress. Evaluation of cancer patient caregiver QOL in Latin America and validation of QOL metrics, such as the Caregiver Quality of Life Index-Cancer (CQOLC), has not yet been done in large populations. We sought to evaluate these characteristics in 5 regions in Colombia. Methods: Cancer patients (n = 165) receiving active treatment and their respective adult caregivers were evaluated. Both caregivers and patients completed a sociodemographic survey, along with the CQOLC, which was translated to Colombian Spanish and validated in a pilot cohort. CQOLC is composed of five subcategories with a total max score of 140. Higher scores are associated with better QOL. Internal consistency was determined by Cronbach’s alpha. Results: The patient’s median age was 63 years (58.8% females). The primary cancer diagnoses were breast, cervical, and lung cancer, with a median ECOG-PS of 1. 6.3% of patients did not have a caregiver, and their responses were also evaluated. The median caregiver age was 53 years (range 19-75 years, 60% females). 4.7% of caregivers were unemployed, and 59% reported financial or psychological distress. 93.8% of caregivers were family members, most frequently spouses or children. The median CQOLC score was 90 ± 15.2. The median score for each of the five subcategories “burden,” “disruptiveness,” “positive adaption,” “financial concern,” and “other” were as follows: 2, 3, 3, 3, and 3 (max score of 4). Conclusions: Most patients and caregivers were interested in participating in the study and reported no issues comprehending or answering the questions. This suggests no potential problems adapting the Spanish-translated CQOLC to future studies. Despite most caregivers reporting financial distress and low family income status, their overall CQOLC scores were relatively high compared to developing countries like the USA, potentially due to cross-cultural differences. The higher median score in the “disruptiveness” category suggests that Colombian caregivers feel strongly committed to caregiving and do not feel this activity interferes significantly with their daily life, possibly related to a sense of family responsibility and moral duty. However, the lower median score in the “burden” category indicates that caregivers feel a heavy emotional toll as a result of their caregiving role. Our results can help identify caregiver QOL areas of improvement, where government policies can be implemented to benefit both the caregiver and the patient.Keywords: caregiver burden, quality of life, Colombia, validation, CQOLC, cancer patients
Extrahepatic cholangiocarcinoma versus intrahepatic cholangiocarcinoma: A comparison of survival outcomes and use of palliative care in diagnosed patients.
Authors: Thakral Nimish, Teresita Gonzalez, Olger Nano, Sang Ha Shin, Shenae Samuels, Atif Mahmoud Hussein
Journal: Journal of Clinical Oncology (2022)

e16192 Background: Cholangiocarcinoma (CCA), a malignancy of the biliary tract epithelium, is of increasing importance due to its rising incidence worldwide. However, it also remains one of the most lethal malignances with a survival rate ranging between 6-16 months. Despite poor outcomes, palliative care remains underutilized in CCA. Determining outcomes, and differences in various CCA types remains crucial in helping patients and clinicians make goal of care decisions with regards to aggressive treatment. Objectives:The objective of this study is to compare survival outcomes between intrahepatic (iCCA) and extrahepatic cholangiocarcinoma (eCCA). In addition, it aims to compare the utilization palliative care in either subtype, considering the high morbidity and mortality of the disease. Methods: Pooled cross-sectional observational study of the2004-2017 National Cancer Database (NCDB), which contains almost 400,000 records. The study population included de-identified records of patients with CCA; ages 18-90. Descriptive statistics (frequency, means, and standard deviations) were used. For survival analyses, the Kaplan-Meier method with log-rank test and a multivariate Cox regression model was used. Results: A total of 53,054 patients with CCA were identified. Of which, 63.4% had iCCA and 36.7% of patients had eCCA. There were statistically significant differences between the two cohorts in regard to sex, race/ethnicity, as well as in Charlson Co-Morbidity score. 65.2% of iCCA patients had advanced clinical stages III/IV as compared to 62.5% of eCCA patients. Higher percentage of iCCA patients had bone metastasis (7.8% vs 4.6 %, p &lt; 0.001), pulmonary metastasis (11.5% vs 7.8%; p &lt;0.001) and tumor size greater than 5 cm (62.1% vs 20.7%, p &lt;0.001) compared to eCCA. Regarding treatment, patients with iCCA were more likely to receive multi-agent chemotherapy (35.0% vs 26.2 %, p&lt;0.001). Although statistically significant differences for primary site surgical intervention (25.5% vs 25.0%, p&lt;0.001), as well as for immunotherapy (6% vs 5.4%, p= 0.048), was found, they were not clinically significant. Patients with eCCA had a higher 90-day mortality (11.4% vs 8.2%, p &lt;0.001), with 21% less likelihood of survival compared to iCCA patients (AOR:0.79, CI:0.74-0.84). Palliative care remained underutilized, with a lower utilization in iCCA (15.7% vs 12.5%, p &lt;0.001). Conclusions: Our study demonstrated that iCCA patients have better survival outcomes compared to eCCA patients. This could be due to biological/genomic differences which warrant future investigation. Future clinical trials could also stratify for the location of CCA. Despite CCA’s poor prognosis, palliative care remained underutilized, with lower utilization rates in iCCA compared to eCCA.